What is the difference between the two properties panels?
The Properties region, or as it is commonly called the Properties panel, holds settings for the 3D view and the active object.
In the picture below of the properties region, all the selection specific items are at the top. The bottom seven in the red box are all settings for the 3D view. The grease Pencil can be either object specific or scene specific.


The Properties window, or Proprieties editor holds the settings for the entire scene and the active object. The first four contexts (aka "tabs"), in the red box, are for the scene and do not change with the active object. All the other tabs, with the exception of the Texture tab are dependent on the active object. The Texture tab, similar to the grease Pencil, can hold settings for more than just the active object.